Carrot root and DNA VCRU Bioinformatics USDA ARS Vegetable Crops Research Unit

This page was last updated on Wednesday, 22-Jan-2014 16:11:26 CST

Installation notes for tRNAscan-SE version 1.3.1 (January 2012)

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Prerequisites

Perl5

Installation

  1. $ cd /programinstallers/
  2. $ wget -N http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz
  3. $ tar -zxvf tRNAscan-SE.tar.gz
  4. $ cd tRNAscan-SE-1.3.1
  5. Edit the top of the Makefile.
    $ nano Makefile
    Set the paths and other make variables to suit your system.
    In particular, you need to specify:
    1. where executables are to be installed
    2. where data files are to be installed
    3. where Perl is already installed on the system
    4. what the Perl binary is called (i.e. 'perl' or 'perl5')
    5. where temporary files will reside
    6. where to install man pages
    PERLDIR = /usr/bin
    PERLBIN = perl
    BINDIR  = $(HOME)/bin
    LIBDIR  = $(HOME)/lib/tRNAscan-SE
    MANDIR  = $(HOME)/man
    TEMPDIR = /tmp

    becomes
    PERLDIR = /usr/bin
    PERLBIN = perl
    BINDIR  =
    /usr/local/bin
    LIBDIR  =
    /usr/local/lib/tRNAscan-SE
    MANDIR  =
    /usr/local/share/man
    TEMPDIR = /tmp

  6. $ make
  7. $ sudo make install
    .
    .
    .
    cp trnascan-1.4 covels-SE coves-SE eufindtRNA tRNAscan-SE /usr/local/bin/.
    cp -R tRNAscanSE /usr/local/bin/
    cp TPCsignal Dsignal *.cm gcode.* /usr/local/lib/tRNAscan-SE/.
    cp tRNAscan-SE.man /usr/local/share/man/man1/tRNAscan-SE.1
  8. Cleanup
    $ cd ..
  9. $ rm tRNAscan-SE-1.3.1 -rf
  10. To correct the error message
    Can't locate tRNAscanSE/Utils.pm in @INC (@INC contains:...
    I patched /usr/local/bin/tRNAscan-SE with the following additional line
    use lib "/usr/local/bin"; # otherwise can't find modules listed below
    inserted at line 28
  11. I also needed to do this (permissions were 754 previously)
    $ sudo chmod 755 /usr/local/bin/tRNAscanSE
  12. And for cgi compatibility, found three system() calls to rm in /usr/local/bin/tRNAscan-SE, changed to use the full path for each of these /bin/rm